The genetic code

Question 1

What does understanding the genetic code allow us to do?

Answer 1

-infer protein sequence from DNA
-infer protein structure from its sequence
-infer protein function by comparison
-design tools to study protein function

Question 2

In which direction does the ribosome move and are the codons read?

Answer 2

-in a 5’ to 3’ direction
-protein synthesis occurs in a N’ to C’ direction

Question 3

What is a cognate tRNA?

Answer 3

tRNA with the same genetic meaning in relation to the amino acid or enzyme that charges it

Question 4

What type of bond forms between adjacent tRNA molecules and where?

Answer 4

Peptide bonds form between aminoacyl + peptidyl groups

Question 5

What bond joins an amino acid to tRNA?

Answer 5

Ester linkage between the 3’ hydroxyl group of the terminal A nucleotide + the amino acid carboxyl group

Question 6

What did Crick and Brenner show?

Answer 6

-genetic code is based on triplet codon sequences
-code in nonpunctuated
-code is degenerate

Question 7

What does it mean that the genetic code is nonpunctuated?

Answer 7

-all nucleotides have a genetic meaning
-there’s no space between codons

Question 8

Describe a ribosome binding assay

Answer 8

-extracted cells can be ‘programmed’ to make protein as they still contain active enzymes
-uses artificial RNA synthesised with polynucleotide phosphorylase
-add amino acid with radioactive label (protein will be radioactive if amino acid taken up)
-poly(U) RNA was shown to specifically direct the incorporation of phenylalanine into the protein

Question 9

What are the main meanings of the 64 codons?

Answer 9

-61 sense codons code for specific amino acids
-3 termination codons (UAA, UAG, UGA)
-initiation codon is almost always AUG and can be found throughout the code

Question 10

What is the N terminal amino acid of proteins?

Answer 10

Methionine as encoded for by the initiation codon

Question 11

What are the 2 amino acids that are encoded by unique codons?

Answer 11

Met and Trp

Question 12

Some synonymous codons are recognised by what?

Answer 12

Different isoacceptor tRNAs that are charged with the same amino acid

Question 13

Describe the structure of tRNA

Answer 13

-cloverleaf secondary structure
-the 5’ and 3’ ends are drawn together
-all tRNAs have the same 3’ terminal nucleotides CAA
-specific nucleotides within tRNAs are post-transcriptionally modified

Question 14

What shape do tRNAs fold into and why?

Answer 14

-into an L shape due to tertiary interactions
-produces a flat, L-shaped molecule where the anticodon loop + aminoacyl group are positioned at opposite ends of the molecule

Question 15

What is coaxial stacking?

Answer 15

Aligning the short helices to form a longer helical structure

Question 16

What does coaxial stacking do?

Answer 16

Increases the thermodynamic stability of RNA

Question 17

What is stacked in coaxial stacking?

Answer 17

-acceptor step is stacked in the T psi C arm
-anticodon is stacked on the D arm
-base pairing occurs between the D and T psi C loops

Question 18

What is tRNA charging mediated by?

Answer 18

-aminoacyl-tRNA synthetase
-reaction requires ATP

Question 19

What are all isoacceptor tRNAs charged by?

Answer 19

A single enzyme